This has been an annoying bug for a while, so I actually just fixed it. The fix will go up to conda with the next release, so for now just be sure you're accounting for the +1 difference between .loci and .vcf when verifying snp status.

@isaacovercast Thanks!! I found out what happened. it turns out that I have many loci with with low frequency sites. When I filtered out sites with MAF>0.01, the few different sites across individuals were removed, leaving me with a bunch of monomorphic loci.